cBioPortal validation report

Study directory:
/datahub/mixed_nfosi_2022

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version 5.1.7-dirty-SNAPSHOT

Validation status: Failed
Line Number Column Number Message Value Encountered
Debug Requesting info from portal at 'http://cbioportal.org'
Debug Requesting cancer-types from portal at 'http://cbioportal.org'
Debug Requesting genes from portal at 'http://cbioportal.org'
Debug Requesting genesets from portal at 'http://cbioportal.org'
Debug Requesting genesets_version from portal at 'http://cbioportal.org'
Debug Requesting gene-panels from portal at 'http://cbioportal.org'
Info No directory named 'case_lists' found, so assuming no custom case lists.
Error No case list found with stable_id 'mixed_nfosi_2022_sequenced', please add this case list to specify which samples are profiled for mutations. This is required for calculation of samples with mutations in OncoPrint and Study Summary.
Info Validation complete
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning Columns OS_MONTHS and/or OS_STATUS not found. Overall survival analysis feature will not be available for this study.
Warning Columns DFS_MONTHS and/or DFS_STATUS not found. Disease free analysis feature will not be available for this study.
Error 21 1 Patient defined multiple times in file JH-2-031 (already defined on line 20)
Info Validation of file complete
Info Read 23 lines. Lines with warning: 0. Lines with error: 1
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 24 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 68 A SWISSPROT column was found in datafile without specifying associated 'swissprot_identifier' in metafile, assuming 'swissprot_identifier: name'.
Info 2, 3, 5… Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA] 3'Flank, Intron, 3'UTR… See all 28811 values
Error 4, 7, 22… 4 The reference genome in column NCBI_Build does not correspond with the reference genome specified for this study (GRCh37) GRCh38 See all 9294 values
Warning 4, 7, 22… SWISSPROT value is not a (single) UniProtKB/Swiss-Prot name. Loader will try to find UniProtKB accession using Entrez gene id or gene symbol. Q9UKB5.139, Q13029.214, Q8N1P7.139… See all 8348 values
Info 27, 52, 53… This variant (Gene symbol 'Unknown', Entrez gene ID 0) will be filtered out IGR See all 2995 values
Warning 44, 162, 163… Missing value in SWISSPROT column; this column is recommended to make sure that the UniProt canonical isoform is used when drawing Pfam domains in the mutations view. See all 939 values
Warning 93, 97, 167… No Amino_Acid_Change or HGVSp_Short value. This mutation record will get a generic "MUTATED" flag See all 653 values
Warning 181, 11042, 18159… SWISSPROT value is not a single UniProtKB/Swiss-Prot name. Found multiple separated by a `,`. Loader will try to find UniProtKB accession using Entrez gene id or gene symbol. A0A0B4J2D9.43,P0DP09.24, P62861.147,P35544.162, P01768.117,P0DP03.21 See all 7 values
Warning 977, 1142, 1143… Gene symbol not known to the cBioPortal instance. This record will not be loaded. ENST00000529081, LMLN2, ENST00000634254… See all 10 values
Info Validation of file complete
Info Read 41101 lines. Lines with warning: 9294. Lines with error: 9294
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Info No reference genome specified -- using default (hg19)

Legend

Click on a filename below to see a table of messages about the data in the file. The colors in the tables have the following meanings:

Error Error: cBioPortal will not know how to load this, please revise or remove
Warning Warning: possible cause of confusion, please check whether this is intended
Info Info: this looks good, no action required
Debug Verbose output: details on the progress of the validation script